Cichlid diversity
The more than 20,000 species of bony fishes represent more than half of all living vertebrates. Among these, the perch-like fishes (Order Perciformes) include more than 9,300 species (Nelson, 1994). A group of laboratories around the world are working together to develop genomic resources for one of the most diverse groups of Perciformes, the family Cichlidae (>1500 species). Cichlids (pronounced 'siklids') are found in tropical regions of the Americas, Africa, Madagascar and Sri Lanka, but achieve their greatest diversity in the Great Lakes of East Africa.

The three major lakes in East Africa (Malawi, Tanganyika and Victoria) each harbor a separate radiation of several hundred species. The radiations in Lakes Malawi and Victoria have occurred in roughly the last million years, making this the most rapid rate of speciation known in vertebrates, and a fascinating system for studying the mechanisms of evolution and speciation. These fishes are also excellent model organisms for studying the genetic and developmental basis for differences in morphology and behavior.

Food fish
Tilapia (Oreochromis spp.) are cichlid fishes which shared a common ancestor with the East African lake flocks about 10 million years ago. They are one of the most important species in aquaculture today, with world-wide production exceeding 1 billion pounds per year. Increasingly popular in western cuisine, tilapia are a particularly important source of protein in less developed countries. Recipes!

Genomic resources
The descriptions and links below will lead you to the genome research tools already developed for studies of these fishes, including genetic linkage maps, cDNA clone libraries, and a physical map based on the restriction fingerprints of 35,000 BAC clones.

Several genetic linkage maps of cichlid fishes have been constructed. Our latest map, based on an interspecific F2 cross between O. niloticus and O. aureus has an average spacing of 3cM between microsatellite markers (Lee et al. 2005)(PDF).

We have also published a map for Lake Malawi cichlids, based on the F2 of an intergeneric cross of two Lake Malawi cichlids (Metriaclima zebra and Labeotropheus fuelleborni). Although this map has fewer markers, we were able to select markers from the tilapia map to fill in gaps. When we compare marker orders in these two maps, we find only two obvious rearrangements, indicating that gene order is largely conserved across this group of fishes.

Four tilapia BAC libraries have been produced at the Tokyo University of Fisheries
(Katagiri et al. 2000) (PDF). Plates and filters for portions of libraries 3 and 4 are available. Contact Tom Kocher for more information.

HCGS has constructed a BAC library for the Lake Malawi cichlid Metriaclima zebra. This library is also available at cost by contacting Tom Kocher (tdk@umd.edu).

A library from the Lake Victoria cichlid Haplochromis chilotes (10x coverage, 128kb average insert size) has been constructed at the Tokyo Institute of Technology by Watanabe et al. (2003). [PDF]

A third haplochromine library, from the Lake Tanganyika species Astatotilapia burtoni (12x coverage, 150kb average insert size), has been constructed by Michael Lang in Chris Amemiya's lab, in a collaboration with Axel Meyer at the University of Konstanz (Lang et al. 2006). (PDF)

With support from the US Dept. of Agriculture, we have fingerprinted more than 35,000 clones from tilapia libraries 3 and 4
(approximately 5x coverage of the genome). The assembled contigs can be viewed on the HCGS FPC viewer.

There are many labs around the world working to develop cDNA resources for cichlids. Hans Hofmann (Bauer Center, Harvard) is organizing a cichlid microarray collaboration. The HCGS has mapped existing ESTs onto the Fugu scaffolds in our comparative mapping viewer.